We now have the raw data, red an green intensities which we have access too

dim(getRed(rgset))

## [1] 622399 6

dim(getGreen(rgset))

## [1] 622399 6

If you are not interested in developing preprocessing algorithms then you can use the built in preprocessing algorithmg and go straight to object that give you access to methylation esimatates

mset<-preprocessIllumina(rgset)

## Loading required package: IlluminaHumanMethylation450kmanifest

This performs the default preprocessing algorithm developed by Illumina. However, for this to be useful we want to have the locations of each CpG and to do that we need map the CpGs to genome. Minfi keeps this information modular so that when the genome annotation gets updated one can easilty change the mapping.